Biodiversity
Informatics Visualization

Project description

We are building information retrieval and analysis interfaces for the rapidly expanding
domain of biodiversity and ecological databases. Biodiversity databases contain
organism-related information such as distribution, taxonomy, natural history,
and conservation data. They are as complex as molecular and medical biology
resources, yet serve a broad audience as do general-use digital libraries. We
began by developing an interactive tree visualization (TaxonTree)
for Kingdom Animalia. We also developed a prototype allowing coupled interaction
with two trees (DoubleTree). We are currently working
on developing other methods of visualizing both hierarchical and
non-hierarchical biodiversity information (TreePlus and EcoLens),
leveraging prior research on digital
libraries and on bioinformatics. This has involved exploring ontologies and biodiversity data management in collaboration with the
Animal Diversity Web
(ADW) and the SPIRE project, and
tree-reasoning with Kevin Omland at UMBC.

Reports and data products

We created this ontology for animal life history and natural history:
ADW Ontology in OWLADW Ontology Protege Project filesPlease note that this is a draft not actually in use by ADW.
It is in revision by the SPIRE project. Please contact Cyndy Parr for more
information.

EcoLens

This platform allows biologists to browse through a large database of information about food webs,
find webs of interest, and then visualize links using TreePlus (see below).
It is essentially a front end to relational data tables that offers coupled
interaction, searching, and simple bar chart visualization to replace complex
queries. EcoLens is a customization of PaperLens, and the next generation
application, NetLens, is more generic and feature-filled.

EcoLens without .NET
if
you
already have Microsoft's .NET Framework installed (670 KB). Run
EcoLensSetup.msi to install.

EcoLens with .NET if you
need
.NET (23 MB). Unzip the file and then run EcoLensSetup-With-dotNet.exe to
install.

Released 12 December 2005. Not compatible with Macintosh. Data reside on an online database so you must
be connected to the internet to use EcoLens. Let us know if this is a
problem for you. These
data, described here, are also being used by the SPIRE project
in different formats to model interactions among organisms and serve as a testbed for semantic web technologies in this domain.

TreePlus

We have developed a new graph visualizer to enable
exploration of large, complex food webs. Ultimately, this system, embedded in ecoLens,
above, will allow biologists to test approaches to modelling interactions among organisms.
While inspired by SpaceTree and TaxonTree, it is an entirely new application
written in C#.

Please see HCIL's TreePlus page for more information, including a video demonstration.

TaxonTree

TaxonTree combines dynamic query interfaces and zoomable graphics to visually
accommodate highly interconnected data such as the Linnaean hierarchy for
Kingdom Animalia . Because the structure of the data is visualized, the
interface should be suitable both for biologists and for the general public.
Names of organisms are essential to any biological database, including genomic
databases, so a tool that allows effective searching and browsing of these names
has wide application.

TaxonTree allows full-text searching and browsing of a large, widely used
multimedia database, University of Michigan's
Animal Diversity Web via a
classification of almost 200,000 animal names. At higher levels, binary
branching illustrates relationships, and synapomorphies supporting those
relationships are also available. Scientific names have been compiled from
ITIS, the
UMMZ Bird Division, the
EMBL Reptile
Database, Mammal Species of the World,
and material from University of Maryland's BSCI 224 course taught by Jeff
Jensen.

Online versions:
As of Summer 2005 you can find TaxonTree behind any "Show in TaxonTree" link
at http://animaldiversity.org. By
using TaxonTree you give us consent to use logs of your use for our research
on information retrieval interfaces. We will not have any personal,
sensitive information about our users. If you do not already have a current
version, download Java.

Stand-alone version: Download:
taxontree-1.2.zip released September 2003 (12 MB). Not compatible with
Macintosh. If you do not already have a current version,
download Java.
To run, double click on the taxontree.jar file. Tree A (from Bioinformatics
paper) is included as taxon.mdb.

DoubleTree

DoubleTree is an an application for comparing two trees using coupled
interaction. DoubleTree is built on TaxonTree.

Stand-alone version: Download:
doubletree-0.7.zip released December 2003 (25 MB) This prototype lacks
many features and has several content bugs but illustrates the basic
concept. . If you do not already have a current version,
download Java. Not
compatible with Macintosh. To run, double click on the doubletree.jar file.
Included are three trees; default settings show a folk tree in the upper
pane (Tree C from Bioinformatics paper), and the combined phylogeny/taxonomy
described above for TaxonTree in the lower pane (Tree A). To swap the folk
tree for an ITIS tree, rename taxon_alt.mdb (Tree B) to taxonA.mdb.

Sponsors

This material is based upon work supported by the National Science
Foundation under ITR Grant No. 0219492. Any opinions, findings, and
conclusions or recommendations expressed in
this material are those of the author(s) and do not necessarily reflect
the views of the National Science Foundation.